ARCHITECTURAL ACCOMMODATION IN THE COMPLEX OF 4 P53 DNA-BINDING DOMAIN PEPTIDES WITH THE P21 WAF1/CIP1 DNA RESPONSE ELEMENT/

High resolution chemical footprinting and cross-linking experiments ha ve provided a basis for elucidating the overall architecture of the co mplex between the core DNA binding domain of p53 (p53DBD, amino acids 98-309) and the p21/waf1/cip1 DNA response element implicated in the G (1)/S phase cell cycle checkpoint. These studies complement both a cry stal structure and earlier biophysical studies and provide the first d irect experimental evidence that four subunits of p53DBD bind to the r esponse element in a regular staggered array having pseudodyad symmetr y, The invariant guanosines in the highly conserved C(A/T)\(T/A)G part s of the consensus half-sites are critical to the p53DBD-DNA binding. Molecular modeling of the complex using the observed peptide-DNA conta cts shows that when four subunits of p53DBD bind the response element, the DNA has to bend similar to 50 degrees to relieve steric clashes a mong different subunits, consistent with recent DNA cyclization studie s. The overall lateral arrangement of the four p53 subunits with respe ct to the DNA loop comprises a novel nucleoprotein assembly that has n ot been reported previously in other complexes. We suggest that this k ind of nucleoprotein superstructure may be important for p53 binding t o response elements packed in chromatin and for subsequent transactiva tion of p53-mediated genes.